Only chief scientist Alex Zelinsky, new associate secretary Rebecca Skinner, and another deputy secretary, Steve Grzeskowiak, remain among top civilian Defence leaders since the end of last financial year.

Mr Gillis was appointed deputy secretary of the department's capability acquisition and sustainment arm, employing more than 5000 people, in August 2015.

Before joining Defence, he was vice president and managing director of Boeing Defence Australia, and he previously worked in the former Defence Materiel Organisation.